Abstract: Abstract：Objectives A fault-tolerant control (FTC) method based on improved adaptive control allocation (IACA) is proposed to enhance propulsion efficiency in over-actuated ships affected by thruster faults. Methods First, the IACA algorithm is designed for real-time adaptive reconstruction of the configuration matrix of the propulsion system in the presence of faults. This process aims to minimize the thrust deviation based on the current propulsion capacity. Additionally, the algorithm incorporates a differential term in the adaptive updating law to mitigate thrust jitter during the adaptation process. On this basis, a modified extended state observer (MESO) is designed to estimate the unprocessed control allocation errors as generalized disturbances within the system and to compensate for them in the control law. Finally, the boundedness error in the closed-loop control system has been proven. Results Simulation and model experiments are conducted using a self-developed over-actuated ship prototype. The results indicate that the proposed method effectively reduces operating errors during thruster faults, enables the system to recover to the stable state more quickly, and mitigates the buffeting phenomenon within the system. Conclusions In summary, the proposed method can effectively address the loss of thruster effectiveness and improve the fault tolerance capabilities of the over-actuated ship during operation. This advancement is significant for improving the safety and reliability of over-actuated ships.